[gmx-users] crystals of KCl during simulation

Rebeca García Fandiño regafan at hotmail.com
Mon Jun 1 17:36:14 CEST 2009

Thank you very much for your answer. I have read some recent literature, and you are right, it is a problem about the parameters for ions in Amber.


I have found this paper:

Parameters of Monovalent Ions in the Amber-99 Forcefield: Assesment of Inaccuracies and Proposed Improvements



There, they simulate nucleic acids using a combination of Amber and OPLS sigma and epsilon for the ions. I have tried that in the case of my protein, just changing the ion sigma and epsilon in the topology by those corresponding to OPLS, but I still observe aggregation for the ions.


Would this combination of Amber and OPLS have any kind of potential problem during the simulation? Has anybody any idea to avoid this type of artefact?


Thank you very much in advance,


> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] crystals of KCl during simulation 
> Date: Mon, 1 Jun 2009 14:34:55 +0200
> From: baaden at smplinux.de
> Hi,
> regafan at hotmail.com said:
> >> [..] but after equilibration I have observed that KCl is aggregating, like
> >> if it was making crystals. When I used NaCl instead KCl, this not
> >> happened.
> >> Does anybody has any idea about the reason of the behaviour of KCl in
> >> the simulation?
> This even does happen with Amber :) So my guess is you correctly transferred
> the parameters, but stumbled upon an artefact. If you check the recent 
> literature you may notice that many publications with Amber using K+ 
> only employ minimal (neutralising) salt conditions as a workaround. At 
> least this is what we did recently [1].
> Marc Baaden
> [1] Interactions between neuronal fusion proteins explored by molecular
> dynamics, Biophys.J.94, 2008, 3436-3446.
> http://dx.doi.org/10.1529/biophysj.107.123117
> -- 
> Dr. Marc Baaden - Institut de Biologie Physico-Chimique, Paris
> mailto:baaden at smplinux.de - http://www.baaden.ibpc.fr
> FAX: +33 15841 5026 - Tel: +33 15841 5176 ou +33 609 843217
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